Science and Technology Platform Program for Advanced Biological Medicine


Protein Structural Analysis by the Extended Crystalline Sponge Method

<Project Leader> FUJITA Daishi

Kyoto University Institute for Integrated Cell-Material Sciences


The crystaline sponge method (CS method: Nature, 2013, 495, 461.) is a new X-ray technique that does not require crystallization of the analyte and has the potential to revolutionize all natural science fields dealing with molecules. In this research, we aim to extend the CS method to enable the analysis of protein molecules using a large crystalline synthetic cage. Expanding the scope of analytes from small molecules to medium and large molecules has been the most substantial request from the pharmaceutical industry, but the synthesis of crystalline molecules capable of encapsulating protein molecules with a diameter of about 10 nanometers has long been a daunting challenge. We have recently developed a new molecular design theory based on mathematics that allows the self-assembly of molecules from more than 100 subcomponents, demonstrating the formation of massive crystalline synthetic molecules close to ten nanometers in diameter (Nature 2016, 540, 563.). Now, we are preparing to extend the CS method to proteins. Our preliminary results have already shown that caged proteins retain their original tertiary structure even with enhanced stability. We will be able to observe and analyze weak and transient protein-ligand interactions by encapsulating the analyte and stabilizing the complex.

Main Research Themes

(1) Development of an extended CS method for protein structure analysis
Until now, the scope of the unique CS method has been limited to small molecules in terms of molecular size. In the future, we will technically expand the scope of the analyte to macromolecules like proteins. This allows us to cover all major drug modalities, from small molecules to peptides, nucleic acids and proteins. I am particularly interested in the analysis of weak or transient protein-ligand interactions.

(2) Application to biomedical research
By extending the scope of analysis to larger molecules, a vertically integrated molecular structure elucidation platform from small molecules to protein structures will be realized. Based on a model scenario of chronic pain drug discovery, we will demonstrate the utility of the technology from small molecule ligand discovery to structural analysis of protein-ligand complexes.

(3) Industrial application and technology transfer
Technological improvements and generalization for joint use are essential. Seamlessly share the developed technology with the consortium members and link it to industrial use. All developed technologies will be transferred to the university’s joint-use organization.

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